Hi,
You may want to try the 'autoimage' command, which typically does the
"right thing" (TM) when it comes to imaging. For multimers, I've often
had success with an 'autoimage' followed with some supplementary
imaging. So in your case assuming a trimer and assuming that A B and C
are molecules 1 2 and 3 something like this may work:
autoimage
center ^1-3
image bymol !(^1-3)
The 'autoimage' command gets things in the right cell and orientation,
then you center on the molecules of interest and re-image everything
that is not those molecules. Hope this helps,
-Dan
On Fri, Oct 2, 2020 at 10:22 AM Ari Zeida <zeidaari.gmail.com> wrote:
>
> Dear Amber users,
>
> I have performed MD simulations on a trimeric protein complex (let's say
> protein A, B and C). I have run the simulations using the iwrap=1 option.
> At a certain point of the dynamics, part of the C protein "got out of the
> box", and now I'm having trouble imaging the resulting trajectories using
> cpptraj. I've tried centering in a sequential way, first protein A, then
> A-B, then A-B-C (that worked for me in the past) without good results. I've
> also followed without success Dan Roe suggestions posted in
> http://archive.ambermd.org/201207/0443.html.
>
> Have you ever had this type of problem? Any suggestion would be appreciated
>
> Thanks
>
> Ari
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Oct 04 2020 - 07:00:03 PDT
